Useful R code 2

## Warning: package 'rmarkdown' was built under R version 3.5.2

 

Date: 2019-09-24
R version: 3.5.0
*Corresponding author: matthew.malishev@gmail.com
This document can be found at https://github.com/darwinanddavis/UsefulCode

Overview

Same deal as Useful Code, but the second instalment because the first one has too much stuff in it and now runs slow.

Colour palettes

Colorspace

require(colorspace)
hcl_palettes(plot = TRUE)  # show all palettes

# https://cran.r-project.org/web/packages/colorspace/vignettes/colorspace.html
require(colorspace)
q4 <- qualitative_hcl(4, palette = "Dark 3")  # discrete
s9 <- sequential_hcl(9, "Purples 3")  # continuous
# for ggplot
scale_color_discrete_sequential(palette = "Purples 3", nmax = 6, order = 2:6)
# for colospace functions: hcl_palettes() %>% str hcl_palettes()['type']

Neon colour palettes

# https://www.shutterstock.com/blog/neon-color-palettes
neon1 <- c("#3B27BA", "#FF61BE", "#13CA91", "#FF9472")
neon2 <- c("#FFDEF3", "#FF61BE", "#3B55CE", "#35212A")
neon3 <- c("#FEA0FE", "#F85125", "#02B8A2", "#535EEB")
neon4 <- c("#535EEB", "#001437", "#C6BDEA", "#FFAA01")
scales::show_col(c(neon1, neon2, neon3, neon4))

D3

D3 and leaflet

devtools::install_github("jcheng5/d3scatter")
library(d3scatter)
library(crosstalk)
library(leaflet)
library(tibble)
# install.packages('httpuv')
require(httpuv)

sd <- SharedData$new(quakes[sample(nrow(quakes), 100), ])

bscols(widths = c(12, 6, 6), filter_slider("stations", "Stations", sd, ~stations), leaflet(sd, width = "100%", 
    height = 400) %>% addTiles() %>% addCircleMarkers(lng = sd$data()[, "long"], lat = sd$data()[, "lat"], 
    stroke = F, fill = T, color = "red", fillOpacity = 0.5, radius = ~mag + 2, label = ~paste0("Depth: ", 
        as.character(depth))), d3scatter(sd, width = "100%", height = 400, ~mag, ~depth, color = ~stations))

Stations

Data frames

Reversing order of rows in dataframe

# df = data.frame
require(tidyverse)
df %>% map_df(rev)

Lists

Transpose list (flip list elements)

l <- list(1:2, 3:4, 5:7, 8:10)
l
b <- data.table::transpose(l)
b

lengths for getting length of list indices

ls = list(rep(list(sample(50, replace = T)), 5))
ls %>% length
ls %>% lengths
lapply(ls, lengths)

Split list into smaller sublists

la = rep(list(1:5), 6)
names(la) = rep(LETTERS[1:3], 2)
u <- length(unique(names(la)))
n <- length(la)/u
split(la, rep(1:n, each = u))

Fill list elements with NAs to match length of longest element

# https://stackoverflow.com/questions/34570860/add-nas-to-make-all-list-elements-equal-length

# for single index list
set.seed(1)
ls = replicate(5, sample(1:100, 10), simplify = FALSE)
names(ls) = LETTERS[1:length(ls)]
lapply(ls, `length<-`, max(lengths(ls)))

# for sublists
ls = list(replicate(5, sample(1:100, 10), simplify = FALSE))
n.ticks = 20
fillvec = function(x) {
    nv = lapply(x, `length<-`, n.ticks)  # fill remaining vec with NAs to match total length
    rapply(nv, f = function(x) ifelse(is.na(x), 0, x), how = "replace")  # replace NAs with 0s
}
lapply(ls, fillvec)  # apply fillvec to list

Loading packages

pacman

require(pacman)
p_load(dplyr, mapdeck)

Read in data

Read in csv data sources directly from web

# link to raw csv link on e.g. github
require(readr)
url <- "https://raw.githubusercontent.com/plotly/datasets/master/2011_february_aa_flight_paths.csv"
flights <- read_csv(url)

Rmarkdown

---

Split page into three columns (displays best in browser).
R code is in Rmd file.

# r plot code
require(ggplot2)
ggplot(mtcars, aes(x = mpg)) + geom_histogram(fill = "skyblue", alpha = 0.5) + theme_classic()

Praise the lord, I was born to travel
Feeling like Slash in front of the chapel
I’m leaned back with the Les Paul
Shit I smoke is like cholesterol
Spilled dressin’ on the vest at the festival
The best of all, had a midget Puerto Rican at my beckon call

Pump the bass in the trunk
It rattled like a baby hand
Except this toy cost 80 grand
And I’m crazy tan, from all the places that I’ve been
Just from writing words with a pen

---

plotly

HTML widget with plotly and crosstalk

require(plotly)
require(tidyr)
require(crosstalk)

m <- gather(mpg, variable, value, -c(year, cyl))
msd <- highlight_key(m, ~variable)
gg <- ggplot(m, aes(factor(year), value)) + geom_jitter(alpha = 0.3) + labs(x = "Year") + theme_classic()

bscols(widths = c(11, rep(5, 2)), filter_select("id", "Select a variable", msd, ~variable, multiple = F), 
    ggplotly(gg, dynamicTicks = "y") %>% layout(margin = list(l = 30)), plot_ly(msd, x = ~jitter(cyl), 
        y = ~value, alpha = ~cyl, linetype = NULL, mode = "markers", hoverinfo = "text", text = ~paste0("Cyl: ", 
            round(cyl), "\n", variable, ": ", value, "\nYear: ", year)) %>% add_markers(alpha = 0.3) %>% 
        layout(xaxis = list(showgrid = F, title = "Cylinder"), yaxis = list(showgrid = F)))

Select a variable